The skull was long, low, and curved so that both extremities were higher than the middle. The premaxilla bones that formed the end of the snout were enlarged to form a wide tip; there were at least four teeth in the right premaxilla and five in the left. The left maxilla (main tooth-bearing bone of the upper jaw) is more complete than the right, and had at least 29 teeth. There was a deep groove along the midline of the nasals and the frontals; the frontals were fused into a single bone, as is seen in other adult mesoeucrocodylians. Unlike derived neosuchians, it had external antorbital fenestrae. Tykowski and colleagues subjected the skull to CT scanning, which revealed internal cavities and air passages, and showed that it had a double-walled secondary palate similar to that of true crocodylians, and similar pneumatic cavities as well.[2]

Tykowski and colleagues performed a cladistic phylogenetic analysis with their new taxon, and found that it grouped with Goniopholis, Sunosuchus, and, most closely, with Eutretauranosuchus in a weakly supported clade, Goniopholididae. They noted that the skull of Calsoyasuchus is very similar to some goniopholid skulls from the younger, Upper JurassicMorrison Formation. Calsoyasuchus pushes back the earliest occurrence of goniopholids from the Late Jurassic into the Early Jurassic, and not only helps to bridge a temporal gap between groups of crocodyliforms, but also a morphological gap. It also implies that some groups of crocodyliforms have long undiscovered histories.[2]